Learn to visualize and interpret structural variants in short-read NGS data using IGV and real sequencing examples
Copy number variants and other structural variants play an important role in human genetics and are frequently associated with both normal genomic variation and disease. However, detecting and interpreting these variants can be challenging, particularly when working with short-read next-generation sequencing (NGS) data.
What you’ll learn
- Recognize the main signals of structural variants in short-read NGS data, including changes in read depth, allele balance, and discordant read pairs..
- Visualize deletions, duplications, inversions, insertions, and translocations in the Integrative Genomics Viewer (IGV)..
- Interpret structural variant patterns in IGV and distinguish true genomic rearrangements from sequencing or alignment artifacts..
- Understand the biological and clinical consequences of structural variants, including haploinsufficiency and gene dosage effects..
- Apply IGV visualization to support structural variant interpretation in research or clinical genomics..
Course Content
- Introduction to the course –> 2 lectures • 3min.
- Understanding paired-end reads and CNVs –> 2 lectures • 4min.
- Detecting structural variants in short-read data – unbalanced SV –> 12 lectures • 41min.
- Detecting structural variants in short-read data – balanced SV –> 8 lectures • 30min.
Requirements
Copy number variants and other structural variants play an important role in human genetics and are frequently associated with both normal genomic variation and disease. However, detecting and interpreting these variants can be challenging, particularly when working with short-read next-generation sequencing (NGS) data.
This course provides a practical introduction to recognizing and interpreting structural variants using the Integrative Genomics Viewer (IGV). It is designed for biologists, clinical genomic analysts, and researchers who want to build confidence in working with NGS data and structural variation.
Throughout the course, you will learn how different structural variants appear in short-read sequencing data and how to recognize their characteristic patterns in IGV. Using real examples, we will explore how to identify signatures of deletions, duplications, inversions, translocations, and other structural events, and how these patterns can support variant interpretation. The course focuses on practical pattern recognition and aims to help you develop a more intuitive understanding of how structural variation appears in sequencing data.
By the end of this course, you will be able to confidently navigate NGS data in IGV, recognize common structural variant signatures, and use visualization as a practical tool for interpreting genomic variation.
Whether you are beginning to explore structural variants or looking to strengthen your analytical skills, this course offers clear, hands-on training tailored for professionals working with genomic data.